fix: cuda utilization

RasmussenLab · Sep 23, 2024 · 852ee3c · 852ee3c
1 parent bdd14d1
commit 852ee3c
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Showing 3 changed files with 7 additions and 16 deletions.
diff --git a/.github/workflows/cli_vamb.yml b/.github/workflows/cli_vamb.yml
@@ -42,7 +42,7 @@ jobs:
         cat outdir_vamb/log.txt
     - name: Run TaxVAMB
       run: |
-        vamb bin taxvamb --outdir outdir_taxvamb --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy taxonomy_mock.tsv -pe 10 -pt 10 -e 10 -q -pq -t 10 -o C --minfasta 200000
+        vamb bin taxvamb --outdir outdir_taxvamb --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy taxonomy_mock.tsv -pe 10 -pt 10 -e 10 -q -t 10 -o C --minfasta 200000
         ls -la outdir_taxvamb
         cat outdir_taxvamb/log.txt
         vamb bin taxvamb --outdir outdir_taxvamb_no_predict --no_predictor --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy taxonomy_mock.tsv -e 10 -q -t 10 -o C --minfasta 200000
@@ -53,10 +53,10 @@ jobs:
         cat outdir_taxvamb_preds/log.txt
     - name: Run Taxometer
       run: |
-        vamb taxometer --outdir outdir_taxometer --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy taxonomy_mock.tsv -pe 10 -pq -pt 10
+        vamb taxometer --outdir outdir_taxometer --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy taxonomy_mock.tsv -pe 10 -pt 10
         ls -la outdir_taxometer
         cat outdir_taxometer/log.txt
-        vamb taxometer --outdir outdir_taxometer_pred --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy outdir_taxometer/results_taxometer.tsv -pe 10 -pq -pt 10
+        vamb taxometer --outdir outdir_taxometer_pred --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy outdir_taxometer/results_taxometer.tsv -pe 10 -pt 10
         ls -la outdir_taxometer_pred
         cat outdir_taxometer/log.txt
     - name: Run k-means reclustering

diff --git a/vamb/__main__.py b/vamb/__main__.py
@@ -240,7 +240,7 @@ def from_args_taxometer(cls, args: argparse.Namespace):
         return cls(
             typeasserted(args.pred_nepochs, int),
             typeasserted(args.pred_batchsize, int),
-            typeasserted(args.pred_batchsteps, list),
+            [],
         )
 
     def __init__(
@@ -1857,15 +1857,6 @@ def add_predictor_arguments(subparser):
         default=1024,
         help=argparse.SUPPRESS,
     )
-    pred_trainos.add_argument(
-        "-pq",
-        dest="pred_batchsteps",
-        metavar="",
-        type=int,
-        nargs="*",
-        default=[],
-        help=argparse.SUPPRESS,
-    )
     pred_trainos.add_argument(
         "-pthr",
         dest="pred_softmax_threshold",

diff --git a/vamb/taxvamb_encode.py b/vamb/taxvamb_encode.py
@@ -824,9 +824,6 @@ def __init__(
         self.tree = _hloss.Hierarchy(table_parent)
         self.n_tree_nodes = nlabels
 
-        if cuda:
-            self.cuda()
-
         self.nodes = nodes
         self.table_parent = table_parent
         self.hierloss = init_hier_loss(hier_loss, self.tree)
@@ -855,6 +852,9 @@ def __init__(
         self.relu = _nn.LeakyReLU()
         self.dropoutlayer = _nn.Dropout(p=self.dropout)
 
+        if cuda:
+            self.cuda()
+
     def _predict(self, tensor: Tensor) -> tuple[Tensor, Tensor]:
         tensors: list[_torch.Tensor] = list()